tests/testthat/test_apps-variant.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

context("Variant apps with example data")

## this tests do take long therefore we only run them if the environment variable RUN_LONG_TEST is set to TRUE
# Sys.setenv(RUN_LONG_TEST=TRUE)

cwd = getwd()

skipLong = function(){
  if (Sys.getenv("RUN_LONG_TEST") == "TRUE"){
    return()
  } else {
    skip("not running lengthy tests")
  }
}

yeastCommonVariantParam = function(){
  param = list()
  param[['cores']] = '8'
  param[['ram']] = '10'
  param[['scratch']] = '10'
  param[['node']] = ''
  param[['process_mode']] = 'DATASET'
  param[['refBuild']] = 'Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18'
  param[['paired']] = 'true'
  param[['strandMode']] = 'sense'
  param[['refFeatureFile']] = 'genes.gtf'
  param[['mail']] = ''
  param[['dataRoot']] = system.file(package="ezRun", mustWork = TRUE)
  param[['resultDir']] = 'p1001/Count_Result'
  return(param)
}

test_that("Variant_Mpileup", {
  skipLong()
  ezSystem("rm -fr /scratch/test_mpileup/*")
  setwdNew("/scratch/test_mpileup")
  param = yeastCommonVariantParam()
  input = EzDataset$new(file=system.file("extdata/yeast_10k_STAR/dataset.tsv", package="ezRun", mustWork = TRUE),
                        dataRoot=param$dataRoot)
  output = list()
  output[['Name']] = 'Mpileup_Variants'
  output[['VCF [File]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants.vcf.gz'
  output[['TBI [File]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants.vcf.gz.tbi'
  output[['IGV Starter [Link]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants-igv.jnlp'
  output[['Report [File]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants'
  output[['Html [Link]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants/00index.html'
  output[['Species']] = ''
  output[['refBuild']] = 'Saccharomyces_cerevisiae/Ensembl/EF4/Annotation/Version-2013-03-18'
  output[['IGV Starter [File]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants-igv.jnlp'
  output[['IGV Session [File]']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54/Mpileup_Variants-igv.xml'
  output = EzDataset$new(meta=output, dataRoot=param$dataRoot)
  param[['name']] = 'Mpileup_Variants'
  param[['region']] = ''
  param[['mpileupOptions']] = '--skip-indels --output-tags DP,DV,DPR,INFO/DPR,DP4,SP'
  param[['callOptions']] = '--multiallelic-caller --keep-alts --variants-only'
  param[['filterOptions']] = '--include "MIN(DP)>5"'
  param[['specialOptions']] = ''
  param[['dataRoot']] = system.file(package="ezRun", mustWork = TRUE)
  param[['resultDir']] = 'p1001/Variant_Analysis_samtoolsmpileup_8617_2015-11-12--12-19-54'
  myApp = EzAppMpileup$new()
  myApp$run(input=input$copy()$subset(1), output=output$copy()$subset(1), param=param)
  setwd(cwd)
})